Hello bindu 

there is pipelines which gives full annotation and you have to short as for your need.Here you need CRISPR reapeats(http://crispr.i2bc.paris-saclay.fr/) and others are you will get from the (https://www.genoscope.cns.fr/agc/microscope/home/). load your genome and find what ever you need.

Regards

vishal

Some suggestions of software to do these tasks:

1. Pseudogenes

RAST (http://rast.nmpdr.org/) or PGAP (http://www.ncbi.nlm.nih.gov/books/NBK174280/) or Prokka (http://www.ncbi.nlm.nih.gov/pubmed/24642063)

2. Genes with function prediction

RAST (http://rast.nmpdr.org/) or PGAP (http://www.ncbi.nlm.nih.gov/books/NBK174280/) or Prokka (http://www.ncbi.nlm.nih.gov/pubmed/24642063)

3. Genes with pfam domains

PfamScan (http://www.ebi.ac.uk/Tools/pfa/pfamscan/help/)

4. Genes with signal peptides

SIGNALP (http://www.ncbi.nlm.nih.gov/pubmed/21959131) or Phobius (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933244/)

5. Genes with transmembrane helices

SIGNALP (http://www.ncbi.nlm.nih.gov/pubmed/21959131) or Phobius (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933244/)

6. CRISPR repeats

See previous reply.

Difficulty in whole genome analysis? - ResearchGate. Available from: https://www.researchgate.net/post/Difficulty_in_whole_genome_analysis [accessed Jun 22, 2016].

Hi Bindu,

Please check the new annotation file of your genome in NCBI. The latest version has added some details about the pseudogenes.Use Blast-cd search (http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi)  a batch mode of COG and pfam search.

Thank you so much Kothari, David and Aditya for your kind responses. I will go through the programmes and will try to figure it out.

Thanks once again

Have a good one

Bindu

Contact  www.Igenbio.com

Prokka will do a lot of what you are asking for https://github.com/tseemann/prokka 

In addition see https://enterobase.warwick.ac.uk/  . You can upload you E.coli genomes and get large scale comparative genomic analysis to other E.coli

Thank you for the inputs Vinayak Kapatral and Andrew D Millard.

Have a good day

Bindu